gi_545778205_gb_U000_114

cmsearch-Rfam

Family :

LSU_rRNA_archaea

Id:

RF02540

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea;

Ontology:

GO:0003735 structural constituent of ribosomeRF02540

Description:

not description

Score:

1848.6

E-value:

0

From sequence:

2729185

To sequence:

2726282

Alignments:

                                                                                                                 NC
                               :::::{{{{,,,,,,{{{{{{{{{{-----{{{,,{{{{.{{{{{{,,,,,,,((((<<<________>>>,,,,,<<<<< CS
               RF02540       1 uauaucgcgcuauuAcgCcgcccgGuGGAUGGCUcGGCU.cGgGcGcCGAuGAaGGgcGuGgCAAGCUgCgAUAAGCccgG 80     
                               +  +U:::: + U A ::::C:CGGUGGAUG:C +GGC: :::G:G CGAUGA:GG:CGUG  AA CUGCGAUAAGC:::G
  gi_545778205_gb_U000 2729185 AGGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAgUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG 2729105
                               **************************************636789************************************* PP

                                                                                                                 NC
                               <---<<<_______>>>.------>>>>>>,,,)))),,,<<<____>>>,,,,,,,,,,,,,,....,<<<<<____... CS
               RF02540      81 GGgAGgcGCAuGcAgcC.uuuGAuCCcggGAUucCCuAAUgGGAauUCCcguuacuuuuuaaac....gcucccuauu... 153    
                               G  AGG:G  +  A:CC UU+ A+CC:::GAUU:CC:AAUGGG A  CCC+ U + UUU  A      +:::::+A U   
  gi_545778205_gb_U000 2729104 GUAAGGUGAUAUGAACCgUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACAcacuAUCAUUAACUgaa 2729024
                               *****************445689****************************888887777776689999999999988999 PP

                                                                                                                 NC
                               ..........>>>>>,,,,,,<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<____>>,,,<<<<<--- CS
               RF02540     154 ..........gggagcGGGAACcCcccGAAuuGAAaCAUCUuAGUAgggGgAGGAaaAGAAAcCAAuuGgGAUgcCgcuAG 224    
                                         ::::: G GAACC::::GAA UGAAACAUCU AGUA::::GAGGAAAAGAAA:CAA +G:GAU:CC:C AG
  gi_545778205_gb_U000 2729023 uccauagguuAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAG 2728943
                               9********9*********************************************************************** PP

                                                                                                                 NC
                               --<<_____>>---->>>>>,,[[[[,,,,~~~~~~,,,,,,,,,,((((------((((------------(((,,,<-< CS
               RF02540     225 UAgcGGCGAgcGAAAgcGgcauAGccCAAA*[34]*uGUugugggccggcuuuaaugcgccuaguuaaugaAgccGAAgUg 333    
                               UAGCGGCGAGCGAA G:GG:  AGCCCA A      UG  +               ::G    + U + ++AG::GAAG :
  gi_545778205_gb_U000 2728942 UAGCGGCGAGCGAACGGGGAGCAGCCCAGA*[ 3]*UGAAU---------------CAGUG--UGUGUGUUAGUGGAAG-C 2728883
                               ******************************...5..66554...............88888..77888899********.* PP

                                                                                                                 NC
                               <<<______>>>>>,,<___>,<<<_______>>>,,,)))------------))))----)))),,,,,,,,,,,<<<<< CS
               RF02540     334 gccUGGAAuggcccgccauAgAGGGUGAuAGcCCCGUAggcguAaucuaaaaggcgcuugagccguuuccaGAGUAcCgcg 414    
                               G CUGGAA+G C:CGC:AUA:AGGGUGA AGCCCCGUA::C +AA +  A A  C::U  +     U   +GAGUA:: C 
  gi_545778205_gb_U000 2728882 GUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAG----CUCGAUGAGUAGGGCG 2728806
                               ************************************************9999999998777....8999************ PP

                                                                                                                 NC
                               <<___..._____>>>>>>>,,,,,,<<<<<_______>>>>>,,]]]],,,,,}}-}}}}.}}-}},,,,,,,,,,,,,, CS
               RF02540     415 ggUUG...GaauUcccgcGgGAAuaugGggGgcAucaaCccCcAAggCUAAAUACguCcCg.AGACCGAUAGcGaAcuAGU 491    
                               GG      G ++UCC G ::GAAUAUGG:GGG A CA CC:CCAAGGCUAAAUAC: C::: :GACCGAUAG+GAAC AGU
  gi_545778205_gb_U000 2728805 GGACAcguGGUAUCCUGUCUGAAUAUGGGGGG-ACCAUCCUCCAAGGCUAAAUACUCCUGAcUGACCGAUAGUGAACCAGU 2728726
                               **76422367788****************997.89999*******************987636****************** PP

                                                                                                            vv   NC
                               ,<<____>>,,,,}}--------------.-----------.--------}-----}}}}}}}}}},,,,,,,<<<<<<<< CS
               RF02540     492 AccGUGAggGAAAGCUGAAAAGuAcCccu.gaaGGGggGUG.AAAAGaGCCUGAAACcgggcgGcgAuagaauggcgcggC 570    
                               ACCGUGAGGGAAAG: GAAAAG+ACCCC+   AGGGG GUG AAAAGA CCUGAAACCG:G:::: A+A   +G  G  GC
  gi_545778205_gb_U000 2728725 ACCGUGAGGGAAAGGCGAAAAGAACCCCGgCGAGGGGAGUGaAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC 2728645
                               *****************************8889999999998899************************************ PP

                                            vv      v v          v v                                 v       v   NC
                               <<-~~~~~~>>>>>>>>>>,,<<<<________>>>>{{{{{{,,,,(((((((((((((,,<<<<--<<<<_____>>>> CS
               RF02540     571 ccg*[61]*ggGucgcgccgUcCGUuUuGAAaaACGggCCgGGGAGUucgcggccguGgCGAGccUAAgggguuuAacccc 706    
                               :CG      G:GU  C  CGU C UUUUG A AA G G:C:G GA UU:::::C:G :GC AG::UAA:: :    A: ::
  gi_545778205_gb_U000 2728644 ACG*[ 7]*GUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGA----AUAGG 2728567
                               *97...8..9***********************************************************954....4669* PP

                                                                                                                 NC
                               -->>>>,,,<<____>>,,,,,~~~~~~~~~~~~,,,,))))))))))))),,[[-[---[[[[[[,,,(((((((((((( CS
               RF02540     707 GaAggCGuAGgGAAAcCGAuaa*[26]**[16]*uggAGuCacggccgcgaGACCaGAAaCCgggCGAUCUaggCccggGC 817    
                               G A::CG+AGGGAAACCGA               U++AGU: C:G:::::AGACC+GAAACC:GG:GAUC AG:C::: GC
  gi_545778205_gb_U000 2728566 GGAGCCGAAGGGAAACCGAG--*[ 7]**[ 6]*UUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGC 2728487
                               ******************96.....9.....*..9********************************************** PP

                                             v    v                     v                  v                     NC
                               ,<<<<---<<<<<<<____>>>>>>>---->>>>,,,,<<<<-<<-<<________>>>>>>>>,,)-))))))))))),< CS
               RF02540     818 AGGgcGAAgccgggcgaAAgcccgguGGAGgcCCGauAggggUgcUGaugUGCAAauCgcccccgUGACccggGccuAGGG 898    
                               AGG::GAAG::::G  AA  C::::UGGAG::CCGA A::G  :: ::  UG AAA:::: C::+UGAC :::G:CU GGG
  gi_545778205_gb_U000 2728486 AGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGA-ACCGACUA-AUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGG 2728408
                               ************************************.*****999.9********************************** PP

                                                                                                     vv        v NC
                               <<_____>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<---<<<-<<<<<<<< CS
               RF02540     899 GcgAAAGgCCAAUCuAGcccGGuaAuAGCUGGUUCCcgcCGAAacggccCgcAggccgacCccggcgGAGgcuGgcggcgg 979    
                               G:GAAAG:CCAAUC A:CC:GG +AUAGCUGGUUC:C:CCGAAA:::::  + :::::+CC:CG::   : C+::::::G 
  gi_545778205_gb_U000 2728407 GUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAA-UUCAUCUCCGGG 2728328
                               *****************************************************************964.55679******* PP

                                            v    vvv        vvv    v             v       vv                      NC
                               ----<<<----<<<<<<<<<<--~~~~~~>>>>>>>>>>--->>->---->>>>>>>>>>>------>>>>>>->,,,<<< CS
               RF02540     980 gGUAGaGCACugaccGggggguu*[18]*cccccCggucaAACuCCGAAcccgccgcCgcCGuAGAagccggGAgucgGgc 1072   
                               GGUAGAGCACUG  ::GG    +      ++ CC::  CAAACU CGAA+ C::::::  :    A+::CG:GAG C+ :C
  gi_545778205_gb_U000 2728327 GGUAGAGCACUGUUUCGGC---A*[21]*AACCCGAUGCAAACUGCGAAUACCGGAGA--AUGUUAUCACGGGAGACACAC 2728237
                               ****************993...2...3..34599********************9987..45566889************* PP

                                                                                                                 NC
                               <<<<<<__._____>>>>>>>>>,,,,<<<______>>>,,,((((.(((---(((------(-((((((----------- CS
               RF02540    1073 gcccgggG.UAAGcccgggcgcCGaGAGGGgaACAACCCAGAccgg.GGUUAAGGuCCCuAAgUgccGGcUAAGUGucAau 1151   
                               G C:G: G UAA  :C:G CG:  AGAGGG+AACAACCCAGACCG: :G:UAAGGUCCC AAGU:::GG:UAAGUG     
  gi_545778205_gb_U000 2728236 GGCGGGUGcUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCcAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG--- 2728159
                               ****9977478888*******************************55*****************************95... PP

                                      v      vv                                                                  NC
                               -----(((-((((((((((-------(((((,<<<--<<<_________>>>-->>><___><---<<______>>->,)) CS
               RF02540    1152 cuaAAGgguGuccccggcCuaAGACAgCggGgaGGUagGCUuAGAAGCAGCcAUCCucUAAgGAgUGCGUAAcAGCUCACc 1232   
                                 AAA:G UGU ::  G C  AGACA:C::GGA GU GGCUUAGAAGCAGCCAUC U:UAA:GA  GCGUAA AGCUCAC:
  gi_545778205_gb_U000 2728158 --AAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACU 2728080
                               ..568**************************************************************************** PP

                                        vv     v                                                                 NC
                               )))---)))))))))))))--------.-----------))))))))))---)))))))<<<<<<<________>>>>>-- CS
               RF02540    1233 cGcCGAGgccgggggCccCgAAAAUGg.aCGGGGCUuAAgCCggccaCCGAuACCccggggcgcgcuuauuaaagcgcgAu 1312   
                               :G:CGAG C  :: GC C:GAA AUG  ACGGGGCU AA:CC:::CACCGA :C::CGG:: : :C  +U+++ G: :   
  gi_545778205_gb_U000 2728079 GGUCGAGUCGGCCUGCGCGGAAGAUGUaACGGGGCU-AAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGU-- 2728002
                               **************************9788888888.89**********************655555555555555555.. PP

                                                    v                                   v                        NC
                               >>,,,,]]]]]]<-<<<<<.<<<<<------<<<<<<<<____>>>>>>>>--->>>>>>>>>>-->,,,,,}}}}}},,, CS
               RF02540    1313 ccgGUAGgcgGGCGucccg.cccGGguaGAAgccgGgccGuGAggcCcgguGGACCgggcgggaauGaaaAUCCcGGcggu 1392   
                               ::GGUAGG:G:GCGU:C:G :   :   GAAG:  :GC:GUGA:GC:  :UGGA:   :C:G:A UG++AAU C:G:C+  
  gi_545778205_gb_U000 2728001 UGGGUAGGGGAGCGUUCUGuAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUA 2727921
                               *******************445688889***************************************************** PP

                                                                                                                 NC
                               ,,,,,,,,,,,,<<<<<<_______>>>>>>{{{{,,,,{{{{,,{{,,,<<<<<<---<<_____>>->>>>>>,,,,,, CS
               RF02540    1393 AGUAgCAGCaaAGuggGGUGAGAAUCCccaCcGCCGaAaGgGCaAGGGUUccccGGCAAuGuUcGUCaGCCggggGUUAGu 1473   
                               AGUA+C G  AA:::GGGUGA AA CCC:::CGCCG AAG::CAAGGGUUCC:: :CAA:GUU +UC:G: ::GGGU AGU
  gi_545778205_gb_U000 2727920 AGUAAC-GAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGU 2727841
                               ****99.66799********************************************************************* PP

                                            v v            v v                                                   NC
                               [[[,<<.---<<<<<<<<<_____>>>->>>>>>---->>,,,<<<<<________>>>>>,,((((((((---------- CS
               RF02540    1474 CGGUCC.UAAggcgggccguAAcucggacccgccGAAaGGGAAgcgGGUUAAUAUUCCcgcgCcgcgggggUaggugcggu 1553   
                               CG: CC UAAG:C :G:C: AA  :G:  : G:CGA +GGGAA:C:GGUUAAUAUUCC:G:+C::: :G::  +G+G    
  gi_545778205_gb_U000 2727840 CGACCCcUAAGGCGAGGCCGAAA-GGCG-UAGUCGA-UGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCG---- 2727767
                               ***76539999999988888777.9995.6789985.799*******************************544422.... PP

                                                      vv v                                               v v   v NC
                               ---------------(((---(((((((((--(((((<<<<<<..________>>>>>>,.,,<<<<-----<<<<<<<<< CS
               RF02540    1554 AacgcaagccuaauucccGACgccucggGgUAggccgggcggg..gcuguCgucccgccu.AAgcgcuuAAgcccggcgag 1631   
                                          AA   ::GAC:   : GG:UA:G::G::CGGG  +C GU GUCCCG::U AA:CG: UA GC: G ::: 
  gi_545778205_gb_U000 2727766 -----------AAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGcgACGGUUGUCCCGGUUuAAGCGUGUAGGCUGGUUUUC 2727697
                               ...........3345888************************995566666669999986277888888888876666666 PP

                                v         v v   v v                                                 v vv         NC
                               -<<<_____>>>->>>>>>>.>>----->>>>,,,,,,,,,,,<____..>,,,,,,,)))))---)))))))))------ CS
               RF02540    1632 agcCGUAAUGgcGcgagccg.ggugAAggcgcgAuugGcuuuccgUaa..ggagagUUcggccgAucCccggggcCCaUGA 1709   
                                 ::  AAU:: G ::: C  :G+  AG:CG:GAU++     C: UA   :G +++  C::C:+AU:CC :   :CCA GA
  gi_545778205_gb_U000 2727696 CAGGCAAAUCCGGAAAAUCAaGGCUGAGGCGUGAUGACGAGGCACUACggUGCUGAAGCAACAAAUGCCCUGCUUCCAGGA 2727616
                               6666667888866666666643567777888888888777777666655588899999*********99887777777788 PP

                                                                                        v             v          NC
                               ---.))).------------)))))))),]]],,}},,,,,<<______>>,}}}},<<<<_______>>>>,}}}},,,{ CS
               RF02540    1710 AAA.ggg.auugggaaugAucccccgcguCCGUACCgAGAaCCGACACAGGUGCcCcugGcUGAGaAGgCcaAGGCgUaUc 1788   
                               AAA ::   ++G +   G U::C: :::+:CGUACC   AACCGACACAGGUG::C  GG: GAGAA :CCAAGGCG + :
  gi_545778205_gb_U000 2727615 AAAgCCUcUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCA-GGUAGAGAAUACCAAGGCGCU-U 2727537
                               87744444666667778889************************************7.*******************86.9 PP

                                                                                                v v              NC
                               {{{-----{{{{{{{{-{{{,,,,,,,,,,,,,,<<<<<---<<____>>---->>>>><<<<<<<<<._______..... CS
               RF02540    1789 GGguauAAcccgggcgAGGgAAuUCGGCAAAuUagccCCGUAccUUcGggAgAAGGggugCCuGcggc.uuggaaa..... 1863   
                               G:G A AAC:CGGG:GA:GGAA+U GGCAAA U+:::CCGUA:CUUCGG:AGAAGG:::GC:::: :    G +A      
  gi_545778205_gb_U000 2727536 GAG-AGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGuAGGUGAGguccc 2727457
                               ***.99*******************************************************99998775433333367788 PP

                                             v v                                                         v       NC
                               ..............>>>>>>>>><___>,,,,,,,[[[[[[[[[,,<<<_________>>>,,<<<<<<<<<--<<<<___ CS
               RF02540    1864 ..............gccgCaGGuCGCAGUGACuAGGGggccCcgACUGUUUAauAAAAACAuAggcccCcGCuAgcCCGaA 1930   
                                              : ::::GUCG AG  AC AG::GGC: C:ACUGUUUA UAAAAACA A:::C :::C+A C:CGAA
  gi_545778205_gb_U000 2727456 ucgcggauggagcuGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAA 2727376
                               888888888888776789999************************************************************ PP

                                   v                                                                             NC
                               _>>>>-->-->>>>>>>>,,((((,<<<--<<<<<<<--<<<----~~~~~~---->>>>>>>>-->>>>><<<<<<____ CS
               RF02540    1931 AGGgcguGUACgGgggccGAcuCCUGcCCAgugccGGUAccuGAAa*[16]*cgAAgggCCgguaAacGgCGgGgGUAACU 2021   
                               AG:G   GUA::: G:::GAC:CCUGCCC GUGCCGG A::U AA       CGAAG::CCGGUAAACGGCGG::GUAACU
  gi_545778205_gb_U000 2727375 AGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAU*[31]*CGAAGCCCCGGUAAACGGCGGCCGUAACU 2727270
                               ********************************************99...9..689************************** PP

                                                                                                                 NC
                               ___>>>>>><___>,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]],,,,}}}- CS
               RF02540    2022 aUGACcCuCuUAAgGUAGCgaAAUaCCUuGcCGgcUaAgUgcCGgCuuGcAUGAAuGGaguAAcgAGggccCCACUGuCCc 2102   
                               AU AC::UC:UAA:GUAGCGAAAU+CCUUG:CGG:UAAGU:CCG:C UGCA GAAUGG:GUAA:GA :GCC:: CUGUC:C
  gi_545778205_gb_U000 2727269 AUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUC 2727189
                               ********************************************************************************* PP

                                                                                                                 NC
                               }}}}}}}}-}}}},,,,,,,,,,,,,<<<<<________>>>>>,,{{{{{{{{-{{{-{{,,,,,,{{{{-{{{{{{{,( CS
               RF02540    2103 cgcccgggacCCggUGAAcuuacugugccgGuGcAcAguCcggcgacccCcggcggGgAGcGAAGACCCcgUgGAgCUUUA 2183   
                               C:CCCG:GAC:C:GUGAA+UU ++ U: C:GUG A+A  C:G : ACCC CGGC+:G: G: AAGACCCCGUG:A:CUUUA
  gi_545778205_gb_U000 2727188 CACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUA 2727108
                               ********************************************************************************* PP

                                       v                 v                                                       NC
                               (((---(((((((,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<<---------<<<<<____>>>>>------ CS
               RF02540    2184 CuGCAGcCugccguUGgggcgcggccgcgggcgcguAGuGUAGguGGGAGccguugaagcccccccuccggggggggugGA 2264   
                               CU: AGC: G:C: UG:::::::: C :::::G+GUAG  UAGGUGGGAG:C UUGAAG+   ::C CC+G::    UGGA
  gi_545778205_gb_U000 2727107 CUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGA 2727027
                               ********************************************************************************* PP

                                                         v                 v                v            v       NC
                               >>>------------>>>>>>>>>>>>>>>>>>>>>>>,,,<<<<._____..........>>>>,,,,,)))))))---- CS
               RF02540    2265 ggCgacaaUGaaACACCacCcgcccgcggccgcgcccCUaACccc.uaaaa..........gggGGACAucggcaGgUGGG 2334   
                               G:CGAC  UGAAA ACCACCC::::: G ::::::::CUAAC::                  ::GGACA :G:C :GUGGG
  gi_545778205_gb_U000 2727026 GCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUgACCCGuaauccggguUGCGGACAGUGUCUGGUGGG 2726946
                               *******************************************99755444567888888899****************** PP

                                                                                                                 NC
                               )))),,<<<<_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((((<<-<<<<<<_______>>>>>>-- CS
               RF02540    2335 CaGUUuGGcuGGGGCggCACgCccccGAAAAgaUAuCggggGcGCCCaAAGgucggCUCAggcGGguCAGAAacCCgccGu 2415   
                               :AGUUUG:CUGGGGCGG: C:CC:CC AAA  +UA+CGG:GG:GC:C AAGGU:GGCU A::C G:UC GA A:C G::G 
  gi_545778205_gb_U000 2726945 UAGUUUGACUGGGGCGGU-CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGG 2726866
                               ******************.************************************************************** PP

                                                              vv               vv                                NC
                               ->><<______>>,,,,)))))),,,,<<<<<<<<<_________>>>>>>>>>,<-<____>->,]],,,,,,,,,,<<< CS
               RF02540    2416 AGAGcGcAAGGgCAAAAGccggccUGACugggccccuaAaagcaaggggcccaGaggcGAAAgccgGGcCUAGCGAACccc 2496   
                                 AG:GCAA G:CA AAGCC:GC+UGACUG:  :C:U A+ G   :G:  :CAG :GCGAAAGC:GG:C UAG GA CC: 
  gi_545778205_gb_U000 2726865 UUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGG---CGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGG 2726788
                               ************************************988765...************************************ PP

                                                                                                                 NC
                               <<-<<<<<_______>>>>>>>>>>,,,,,...,,,,}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<______ CS
               RF02540    2497 cguGcCcccuuggUGggGgCcggggAuGAC...AGAAAAGcUACCccgGGGAUAACaGagucgucgCgGGCgAGAGcuCau 2574   
                               :G G  C:    G  :G  CC: :G U A    A AAAAG:UAC:CCGGGGAUAACAG::U :U::CG: C+AGAG+UCAU
  gi_545778205_gb_U000 2726787 UG-GUUCUGAAUGGAAGGGCCAUCGCUCAAcggAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAU 2726708
                               **.999999999999**********987753337789******************************************** PP

                                                                                                                 NC
                               _>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<--<<<<<______>>>>>---->>,<<<<<_____>> CS
               RF02540    2575 AUCGACCCcGcgguUugcuACcUCGAUGUCgGcucuccCcAUCCUGGcgguGCAGcAgccgCCAAGGGUcgGGcUGuUCgC 2655   
                               AUCGAC :CG::GUU:G::ACCUCGAUGUCGGCUC::C CAUCCUGG: :UG AG AG: :CCAAGGGU::GGCUGUUCGC
  gi_545778205_gb_U000 2726707 AUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGC 2726627
                               ********************************************************************************* PP

                                                                                                                 NC
                               >>>,,,,,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}}}}},,,,((((((((-- CS
               RF02540    2656 CcgUUAAAgGggaaCgUGagCuGGGUUuAGacCGuCGuGAGaCAGguCGGuugCUacCcgccgGgggUGuugGccGcCUGA 2736   
                               C::UUAAAG G::ACG GAGCUGGGUUUAGA:CGUCGUGAGACAG:UCGGU :CUA:C:GCCG GGG G UGG::::CUGA
  gi_545778205_gb_U000 2726626 CAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGA 2726546
                               ********************************************************************************* PP

                                     v                             v                                             NC
                               ((((,,<<<<<<<<_______________>>>>>>>><<<<<---<<<----<<<<<<<<<<.____.>>>>>-->>>>>- CS
               RF02540    2737 gGGgAAGgcgccccUAGUACGAGAGGAACggggcgcCgggGCCuCugGUgUAcCGGuuGuCc.Gaua.gGgCaaugCCGgG 2815   
                               GGGG   :: C:CCUAGUACGAGAGGA CGG:G ::+:G:::C+CU:GUGU C:GGUUGUC: G +A :GGCA UGCC:GG
  gi_545778205_gb_U000 2726545 GGGGGG-CUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAuGCCAaUGGCACUGCCCGG 2726466
                               ****86.******************************************************85655558************ PP

                                                                                                                 NC
                               --->>>->>>>>,,.<<<----<<<<<___________>>>>>---->>>,))))------)))))))),........... CS
               RF02540    2816 cAGCcacGCcccaa.gggaUAAggGCUGAAaGCAUCUAAGCccGAAacccucCCcGAAAAgAGgCggCcu........... 2884   
                               +AGC:A :::C: A  :GAUAAG:GCUGAAAGCAUCUAAGC:CGAAAC:  CCCCGA A GAG::::CC            
  gi_545778205_gb_U000 2726465 UAGCUAAAUGCGGAaGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCugacccuuuaa 2726385
                               ***********98889***************************************************************** PP

                                           vv                             vv                                 vv  NC
                               .....,,,,,((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<--<______>-->>>>>>--->>>- CS
               RF02540    2885 .....gauuAgGgcccccgUAgAAGAcggggUuGAUgGggcgGgGGUGuAAgccccgAGguuaauCGAggggcuuAGCCcg 2960   
                                     + +AGG  C:: G AGA GAC ::GUUGAU:G::CGG  GUGUAA:C:C:  G      CGA:G:G:U AGC  +
  gi_545778205_gb_U000 2726384 gggucCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCA--G------CGAUGCGUUGAGCUAA 2726312
                               *****999***********************************************9..9......9*************** PP

                                           vv                 NC
                               >>>>>->>>,,,)))),,,,,}}}}::::: CS
               RF02540    2961 CcgccaCcAAuagcCcgAaugcgcgauauu 2990   
                               CCG::AC:AAU   CCG  +G::::A+  U
  gi_545778205_gb_U000 2726311 CCGGUACUAAUGAACCGUGAGGCUUAACCU 2726282
                               ****************************** PP

>>

RNAfold

>gi_545778205_gb_U000_114
UGAAAAUCUUCUCUCAUCCGCCAAAACAGCUUCGGCGUUGUAAGGUUAAG
CCUCACGGUUCAUUAGUACCGGUUAGCUCAACGCAUCGCUGCGCUUACAC
ACCCGGCCUAUCAACGUCGUCGUCUUCAACGUUCCUUCAGGACCCUUAAA
GGGUCAGGGAGAACUCAUCUCGGGGCAAGUUUCGUGCUUAGAUGCUUUCA
GCACUUAUCUCUUCCGCAUUUAGCUACCGGGCAGUGCCAUUGGCAUGACA
ACCCGAACACCAGUGAUGCGUCCACUCCGGUCCUCUCGUACUAGGAGCAG
CCCCCCUCAGUUCUCCAGCGCCCACGGCAGAUAGGGACCGAACUGUCUCA
CGACGUUCUAAACCCAGCUCGCGUACCACUUUAAAUGGCGAACAGCCAUA
CCCUUGGGACCUACUUCAGCCCCAGGAUGUGAUGAGCCGACAUCGAGGUG
CCAAACACCGCCGUCGAUAUGAACUCUUGGGCGGUAUCAGCCUGUUAUCC
CCGGAGUACCUUUUAUCCGUUGAGCGAUGGCCCUUCCAUUCAGAACCACC
GGAUCACUAUGACCUGCUUUCGCACCUGCUCGCGCCGUCACGCUCGCAGU
CAAGCUGGCUUAUGCCAUUGCACUAACCUCCUGAUGUCCGACCAGGAUUA
GCCAACCUUCGUGCUCCUCCGUUACUCUUUAGGAGGAGACCGCCCCAGUC
AAACUACCCACCAGACACUGUCCGCAACCCGGAUUACGGGUCAACGUUAG
AACAUCAAACAUUAAAGGGUGGUAUUUCAAGGUCGGCUCCAUGCAGACUG
GCGUCCACACUUCAAAGCCUCCCACCUAUCCUACACAUCAAGGCUCAAUG
UUCAGUGUCAAGCUAUAGUAAAGGUUCACGGGGUCUUUCCGUCUUGCCGC
GGGUACACUGCAUCUUCACAGCGAGUUCAAUUUCACUGAGUCUCGGGUGG
AGACAGCCUGGCCAUCAUUACGCCAUUCGUGCAGGUCGGAACUUACCCGA
CAAGGAAUUUCGCUACCUUAGGACCGUUAUAGUUACGGCCGCCGUUUACC
GGGGCUUCGAUCAAGAGCUUCGCUUGCGCUAACCCCAUCAAUUAACCUUC
CGGCACCGGGCAGGCGUCACACCGUAUACGUCCACUUUCGUGUUUGCACA
GUGCUGUGUUUUUAAUAAACAGUUGCAGCCAGCUGGUAUCUUCGACUGAU
UUCAGCUCCAUCCGCGAGGGACCUCACCUACAUAUCAGCGUGCCUUCUCC
CGAAGUUACGGCACCAUUUUGCCUAGUUCCUUCACCCGAGUUCUCUCAAG
CGCCUUGGUAUUCUCUACCUGACCACCUGUGUCGGUUUGGGGUACGAUUU
GAUGUUACCUGAUGCUUAGAGGCUUUUCCUGGAAGCAGGGCAUUUGUUGC
UUCAGCACCGUAGUGCCUCGUCAUCACGCCUCAGCCUUGAUUUUCCGGAU
UUGCCUGGAAAACCAGCCUACACGCUUAAACCGGGACAACCGUCGCCCGG
CCAACAUAGCCUUCUCCGUCCCCCCUUCGCAGUAACACCAAGUACAGGAA
UAUUAACCUGUUUCCCAUCGACUACGCCUUUCGGCCUCGCCUUAGGGGUC
GACUCACCCUGCCCCGAUUAACGUUGGACAGGAACCCUUGGUCUUCCGGC
GAGCGGGCUUUUCACCCGCUUUAUCGUUACUUAUGUCAGCAUUCGCACUU
CUGAUACCUCCAGCAUGCCUCACAGCACACCUUCGCAGGCUUACAGAACG
CUCCCCUACCCAACAACGCAUAAGCGUCGCUGCCGCAGCUUCGGUGCAUG
GUUUAGCCCCGUUACAUCUUCCGCGCAGGCCGACUCGACCAGUGAGCUAU
UACGCUUUCUUUAAAUGAUGGCUGCUUCUAAGCCAACAUCCUGGCUGUCU
GGGCCUUCCCACAUCGUUUCCCACUUAACCAUGACUUUGGGACCUUAGCU
GGCGGUCUGGGUUGUUUCCCUCUUCACGACGGACGUUAGCACCCGCCGUG
UGUCUCCCGUGAUAACAUUCUCCGGUAUUCGCAGUUUGCAUCGGGUUGGU
AAGUCGGGAUGACCCCCUUGCCGAAACAGUGCUCUACCCCCGGAGAUGAA
UUCACGAGGCGCUACCUAAAUAGCUUUCGGGGAGAACCAGCUAUCUCCCG
GUUUGAUUGGCCUUUCACCCCCAGCCACAAGUCAUCCGCUAAUUUUUCAA
CAUUAGUCGGUUCGGUCCUCCAGUUAGUGUUACCCAACCUUCAACCUGCC
CAUGGCUAGAUCACCGGGUUUCGGGUCUAUACCCUGCAACUUAACGCCCA
GUUAAGACUCGGUUUCCCUUCGGCUCCCCUAUUCGGUUAACCUUGCUACA
GAAUAUAAGUCGCUGACCCAUUAUACAAAAGGUACGCAGUCACACGCCUA
AGCGUGCUCCCACUGCUUGUACGUACACGGUUUCAGGUUCUUUUUCACUC
CCCUCGCCGGGGUUCUUUUCGCCUUUCCCUCACGGUACUGGUUCACUAUC
GGUCAGUCAGGAGUAUUUAGCCUUGGAGGAUGGUCCCCCCAUAUUCAGAC
AGGAUACCACGUGUCCCGCCCUACUCAUCGAGCUCACAGCAUGUGCAUUU
UUGUGUACGGGGCUGUCACCCUGUAUCGCGCGCCUUUCCAGACGCUUCCA
CUAACACACACACUGAUUCAGGCUCUGGGCUGCUCCCCGUUCGCUCGCCG
CUACUGGGGGAAUCUCGGUUGAUUUCUUUUCCUCGGGGUACUUAGAUGUU
UCAGUUCCCCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGU
GUGUCGAAACACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGG
UUCAUAUCACCUUACCGACGCUUAUCGCAGAUUAGCACGUCCUUCAUCGC
CUCUGACUGCCAGGGCAUCCACCGUGUACGCUUAGUCGCUUAACCUCACA
ACCCGAAGAUGUUUCACUUCAGAGUUGCGAAAAUUUGAG
.......(..((((.........(((((.((((((.(((((.(((((((((..(.((((........))))((.(((.((.((...)).)).))).)).....((((........)))).(((.....))).........((((((...))))))..((((((((......(((((.((....(((((..((.....)))))))....))....((((((.......((((..(((((...))))).....)))).........))))))....(((((((.(....).))).))))..)))))....))))))))((((..(((((..(((((((((.((((.(((....))))))).......((((((.(((.........(((((.....)))))..((((((((((((((..(((.((((..(((...(((((((((((((((((........)))).))))).(((.((...(((((((............((..((((..........))))..))((((.(((.....(((...((.((...)).))...)))....))).))))..((((..(((......)))..))))....((((((....))))..)).((((..(((((.........)))))))))............(((((((...........)))))))))))))).))))).(((((((....(((...)))....(((((.....)))))....(((.((...)).)))......)))))))........))))))))...)))..)))).....(((((.((.(((((....................)))))...))...)))))...)))..)))..)))))).((((....(((((.(((((.((((((...(((..(((((((..((((((((.......)))).)))).))))))))))...(((.........)))))))))))))).)))))....)))).)))))...............((((((((((((...((((.((.((...(((((((((.(((((.((((((((((((((.......((((((...((((((((((((..((((((((......)).(((((........)))))(((((....(((((...........))))))))))..((((((.(((.......))).))))))(((..(((((((((.(((.............((((.((((....)))).))))(((......)))...............))).))))))..)))...))).........)))).))....)))))))...))))).....)))))).....((.((((..(((((.....(((((((.(((((...(((((.....((((....))))..(((....)))..(((....)))((((((((......))))))))..(((......)))....(((((.(.......)))))).)))))..)))))))...........((((......((((((.(((((........))))).......((....))....((((((((......)))))))).....((((..(((((....))))).))))....))))))......))))(((((.......)))))..............((((((.(........)))))))..)))))...)))))..))))))....))))))).....))).))))..................(((((((......((.((..(((((((.(((.(((((((((((((......(((((.((.(((((((..(((((((......)))........(((.(((((.......))))).)))...(((((((((((((.(((..(((.(((........))).)))...(((((((.((((((((.((.(((((......)))....(((.((((.((........)))))))))...(((((((...(((.((((((.....(.((...((((.(..((((((((..(((....))).))))))))..).)))).)).)..)))))))))...))))).)).((((......))))...(.((((((........)))))).)..((((((((............))))...)))).((((((((........))))).)))...)).)).)))))))).))..)))))............(((.(((((((((.(((((..((((((((..((...((........))...))..))))))))...)))..(((((....(((((.((..........)).)))))..)))))((((((.............(((((((((..(((((....))))).....)))))..))))((((.(((....((((...........((((.....))))........))))......).)))))).(((.....)))))))))...)).).)))))))).))).))).)))))..........)))))((((((...)))))).))).))))..))))).))...)).))))).....)))).)))))))))..))).))))))).)))).......)))))))................))))).))))))))))).)).(((((...((.....))...)))))((((((.(((((((.........((((((.(((..((....)))))..))))))........)))))))...)))))).........((((((((....))))))))(((((((......))))))))))).)))))))))))).........)))))).)))....((......))..)))))).)))(((.(((.....)))))).....)))))..))))..)..))))))))).))))))))))).)))))......))))..)............ (-901.80)

Length sequence

: 2989

Length match:

2902